Plant defense signaling peptides and applications thereof

ABSTRACT

The present invention related to a novel plant defense signaling peptide and applications thereof.

RELATED APPLICATION

This application claims priority to U.S. Provisional Application No. 62/068,987, filed on Oct. 27, 2014, the content of which is hereby incorporated by reference in its entirety.

TECHNOLOGY FIELD

The present invention relates to a novel plant defense signaling peptide and applications thereof.

BACKGROUND OF THE INVENTION

All multicellular organisms have evolved mechanisms to perceive and respond to extracellular chemical signals. Among them, peptides are the most common mediators of intercellular interactions in animals because they provide great variety in their sequences, lengths and/or post-translational modifications (PTMs) to represent different physiological responses (Boller, 2005). In contrast to peptide discovery in animals, only a few signaling peptides have been identified in plants (Farrokhi et al., 2008a; Butenko et al., 2009). It is expected that most of the endogenous plant signaling peptides that play prominent roles in intercellular communication are still undiscovered. Because the complete sequencing of the Arabidopsis genome has revealed that plants have up to ten times as many predicted peptide receptors (Shiu and Bleecker, 2003) and transporters (Initiative, 2000) as animals. Moreover, among the currently identified peptides in plants, only relatively few have been found to function in defense signaling. This is mainly due to the fact that defense signaling peptides are mostly derived from the selective action of proteases on larger precursor proteins, are expressed at low levels, and are highly dynamic.

It is already known that tomato wounding can induce an anti-herbivore response, which is regulated by the peptide hormone systemin, and the small molecule hormone jasmonic acid (JA) and its methyl ester, MeJA (Pearce et al., 1991; Orozco-Cardenas et al., 2001). Systemin was the first identified signaling peptide and also the first confirmed peptide elicitor of damage associated molecular patterns (DAMPs) in plant. It is expected that several signaling peptides are involved in combating herbivore and pathogen attack (Cheong et al., 2002; Francia et al., 2007; Chassot et al., 2008), but the details of the regulation of anti-herbivore and anti-pathogen responses by peptides during wounding stress still await elucidation. Several DAMP peptides have been discovered in other plant species and suggested to be bioactive in tomato (Boller and Felix, 2009b; Campos et al., 2014); these include HypSys (Pearce et al., 2001a; Narvaez-Vasquez et al., 2007), RALF (Pearce et al., 2001b) and Pep1 (Huffaker et al., 2006; A. P. Trivilin, 2014). Pep1 was clearly identified to be pathogen-related in Arabidopsis and its putative precursor in tomato was recently found to involve in the anti-pathogen response (A. P. Trivilin, 2014). However, its endogenous level in tomato has not yet been proved to be induced by tissue damage or MeJA, a potent inducer of systemic wound signaling and response in tomato (Scheer and Ryan, 1999). To our knowledge, no study to date has quantitatively profiled the global change in cellular peptide expression in plants before and/or after the induction of stress responses.

There is a need to identify new defense signaling peptides in plants which not only to advance plant stress biology, but also to aid in the development of alternative ways to improve stress tolerance or resistance for better crop productivity and minimization of the use of agrochemicals (Pearce et al., 1991; Pearce et al., 2001a; Huffaker et al., 2006).

SUMMARY OF THE INVENTION

In this invention, it is unexpectedly found that a peptide elicitor derived from tomato pathogenesis-related protein 1 (PR-1) can regulate plant immune responses against biological threats e.g. pathogen infection, which contains a conserved 11-amino acid signaling peptide motif (PxGNxxxxxPY) (SEQ ID NO: 1) across many plant species. It is found that a peptide having such motif acts as a plant defense signaling peptide, which can increase plant defense activity by increasing immune responses such as production of H₂O₂ or plant hormones or activation of one or more anti-herbivore or anti-pathogen genes when applied to plant. It is also found that a CNYx motif is critical to be recognized by an endogenous protease to cleave a precursor (e.g. a full length of PR-1) to generate an active plant defense signaling peptide. Therefore, a peptide with a 15-amin acid motif (CNYxPxGNxxxxxPY) (SEQ ID NO: 28) can also be applied to plant where a plant defense signaling peptide (with the PxGNxxxxxPY motif, SEQ ID NO: 1) can be generated through a specific cleavage by an endogenous protease. Further, a peptide having a CNYx motif (SEQ ID NO: 55) but lacking the 11-amino acid signaling peptide motif (PxGNxxxxxPY) (SEQ ID NO: 1) can be used as a negative regulator to down regulate the defense activity in plants.

Therefore, in one aspect, the present invention provides an isolated plant defense signaling polypeptide comprising an 11-amino acid motif of SEQ ID NO: 1 (PxGNxxxxxPY).

In some embodiments, the plant defense signaling polypeptide of the invention is selected from the group consisting of SEQ ID NO: 2-27.

The present invention also provides an isolated plant defense signaling polypeptide comprising a 15-aurin acid motif of SEQ ID NO: 28 (CNYxPxGNxxxxxPY).

In some embodiments, the plant defense signaling polypeptide of the invention is selected from the group consisting of SEQ ID NO: 29-54.

In another aspect, the present invention relates to a composition comprising a plant defense signaling polypeptide as described herein.

In still another aspect, the present invention relates to a method for treating a plant to increase plant defense activity, comprising applying to said plant a plant defense signaling polypeptide or a composition comprising a plant defense signaling polypeptide as described herein.

In some embodiments, the defense activity includes anti-herbivore or anti pathogen responses, for example, production of hydrogen peroxide (H₂O₂), generation of a plant hormone, e.g. jasmonate (JA), JA conjugated with amino acid isoleucine (JA-Ile) or salicylic acid (SA), or expression of an anti-herbivore or anti-pathogen protein, e.g. proteinase inhibitor 1 (PI-1), proteinase inhibitor 2 (PI-2), pathogenesis-related protein 1b (PR-1b, CAPE1 precursor gene), beta-1,3-glucanase (PR-2), cys protease (PR-7), class ii chitinase (Chi2;1), ethylene response factor 5 (ERF5) or avrpto-dependent pto-interacting protein 3 (Adi3).

In some embodiments, the defense activity is not only exist in local treated site, but also systemic untreated leaves, for example, generation of a plant hormone, salicylic acid (SA), or expression of anti-pathogen proteins, e.g. pathogenesis-related protein 1b (PR-1b, CAPE1 precursor gene) and ethylene response factor 5 (ERF5).

In some embodiments, the CNYx is a core structure for designing protease inhibitor to prevent processing and decrease defense activity.

In some embodiments, the plants to which the inventive method can be applied include both monocotyledon and dicotyledon. Examples of monocotyledon includes but not limited to rice, barley, wheat, rye, oat, corn, bamboo, sugar cane, onion, leek and ginger. Examples of the dicotyledons include, but are not limited to Arabidopsis thaliana, eggplant, tobacco plant, red pepper, tomato, burdock, crown daisy, lettuce, balloon flower, spinach, chard, potato, celery, carrot, water dropwort, parsley, Chinese cabbage, cabbage, radish, watermelon, melon, cucumber, pumpkin, gourd, strawberry, soybean, mung bean, kidney bean, and pea.

In some embodiments, the plant defense signaling polypeptide is present in the composition at a concentration of about 50 nM or more, 100 nM or more, 150 nM or more, 200 nM or more or 250 nM or more.

In some embodiments, the plant defense responses can be induced within 2 hours and last for more than 24 hours after the composition is sprayed to a plant.

In some embodiments, the defense signaling polypeptide of the invention can be applied in combination with salt treatment to enhance the anti-pathogen activity. Therefore, also provided is a combination comprising the defense signaling polypeptide as described herein and salt, and a method of the present invention as described herein can further comprise treating the plant with salt, in addition to applying the defense signaling polypeptide as described herein to the plant. In certain embodiments, the defense signaling polypeptide is mixed with a proper amount of salt and the mixture (in a form of solution or powder) is applied to the plant, e.g. by spray or immersion. A certain example of the salt is NaCl, at a concentration of around 25 mM or more, 50 mM or more, 100 mM or more, 150 mM or more.

In a further aspect, the present invention relates to a method of down regulating a defense activity in a plant, comprising treating the plant with a peptide having a CNYx motif but lacking a 11-amino acid signaling peptide motif (PxGNxxxxxPY) in an amount to effectively reduce or block the enzymatic activity of a protease in cleaving a precursor peptide (e.g. CNYxPxGNxxxxxPY or the full length of PR-1) to generate a plant defense signaling peptide having the 11-amino acid motif of PxGNxxxxxPY as described above.

The details of one or more embodiments of the invention are set forth in the description below. Other features or advantages of the present invention will be apparent from the following detailed description of several embodiments, and also from the appending claims.

BRIEF DESCRIPTION OF THE DRAWINGS

The foregoing summary, as well as the following detailed description of the invention, will be better understood when read in conjunction with the appended drawings. For the purpose of illustrating the invention, there are shown in the drawings embodiments which are presently preferred. It should be understood, however, that the invention is not limited to the precise arrangements and instrumentalities shown.

In the drawings:

FIG. 1 shows validation of the endogenous CAPE1 identity and the expression level triggered by wounding and wounding plus MeJA. The quantitative analysis of endogenous CAPE1 expression level in unwounded (UW), mechanically wounded (MW) and wounded plus MeJA (W) treated tomato using LC-SRM-MS. The data represented the means and SD of three biological samples. The statistically significant differences between the UW, MW and W samples are indicated with *** (P<0.001) based on Student's t-test.

FIG. 2 shows study of CAPE1 bioactivities in the triggering of leaf tissue H₂O₂ production. Detached tomato leaves were treated with water (Control), mechanical wounding (MW), 1.25 mM MeJA, 250 nM systemin and 250 nM CAPE1 peptide for 4 hours, respectively. After the treatment, 1 mg/ml of diaminobenzidine (DAB) was applied to visualize H₂O₂ accumulation. Experiments were presented by three biological repeats to confirm for obtaining the similar results.

FIG. 3 shows anti-pathogen and anti-herbivore defense genes of tomato plants induced by spraying with CAPE1. Relative expression of anti-herbivore and anti-pathogen defense genes were quantified by comparing the expression levels in untreated plants with plants treated with water or 250 nM CAPE1 for 4, 8, and 24 hours (n=5 for each time point). The internal control EF-1α was used for normalization. All statistically significant differences between the CAPE1- and water-treated samples are indicated with * (P<0.05), ** (P<0.01) or *** (P<0.001) based on Student's t-test.

FIG. 4 shows anti-herbivore and anti-pathogen defense responses of tomato plants induced by spraying with CAPE1. (a) Changes of the larval sizes after feeding with water or 250 nM CAPE1 treated tomato leaves. The larval weights of thirty larvae were recorded each day. (b) The Pst DC3000 infection phenotypes of the plants presprayed with water or 100 nM CAPE1 peptide for 2 hours (n=3) prior to pathogen inoculation. The bacterial numbers, presented as log colony-forming units (Log CFU) per g leaf tissue, represent the means and SD of three biological samples. All statistically significant differences between the CAPE1- and water-treated samples are indicated with * (P<0.05) or *** (P<0.001) based on Student's t-test.

FIG. 5 shows induction of jasmonate hormone accumulation by CAPE1 and systemin in excised plants. The level of JA and JA-Ile induced by CAPE1 and systemin. The plants treated with 10 mM phosphate buffer (buffer), 365 nM systemin (Sys) or 365 nM CAPE1 in buffer through the cut stem for 2 and 4 hours (n=3). The quantity of IA and JA-Ile were quantified by LC-SRM-MS and calculated by the abundance of spiked standard II₂JA. Data represent the means and SD of three independent biological replicates. A statistically significant difference compared with the correspondingly treated water (or buffer) samples is indicated with ** (P<0.01) or *** (P<0.001) based on Student's t-test.

FIG. 6 shows the SA accumulation, anti-pathogen genes and responses induced by CAPE1 and flg22 in tomato. (a) The level of SA induced by CAPE1 and flg22. The excised plants were pretreated with 10 mM phosphate buffer (buffer) or 365 nM CAPE1 or 365 nM flg22 in buffer through the cut stem for 8 hours (n=3). The quantity of SA was quantified by LC-SRM-MS and calculated based on the abundance of spiked SA isotopic standard (d₆-SA). (b) The relative expression of WRKY53 and PR-1b were quantified by comparing the expression levels in untreated detached leaves with the detached leaves treated with water, 250 nM CAPE1 or 250 nM flg22 for 2 hours (n=4). The internal control Ubi3 was used for normalization. (c) The Pst DC3000 infection phenotypes for plants presprayed with water, 100 nM CAPE1 or 100 nM flg22 peptide for 2 hours (n=3) prior to the pathogen inoculation. The infection symptoms were observed 4 days after inoculation. The bacterial numbers were calculated 4 days after inoculation and represented as log colony-forming units (Log CFU) per g leaf tissue. Data represent the means and SD of three biological samples. A statistically significant difference compared with the correspondingly treated water (or buffer) samples is indicated with ** (P<0.01) or *** (P<0.001) based on Student's t-test.

FIG. 7 shows CAPE1 can trigger the systemic immune response in tomato. The plants were separated to local and systemic leaves, the systemic leaves were covered by plastic bags to prevent treatment and the local leaves were treated with water or 250 nM CAPE1 for 24 hours. (a) The levels of SA were induced by CAPE1 in local and systemic tomato leaves. The quantities of SA were quantified by LC-SRM-MS and calculated by the abundance of spiked standard d6SA. (b) The relative expression of ERF5 and PR-1b was quantified by comparing the expression levels in untreated leaves with leaves treated with water, 250 nM CAPE1 for 24 hours. The internal control Ubi3 was used for normalization.

FIG. 8 shows identification of conserved CAPE sequences and proproteins in diverse species based on tomato CAPE1. (a) The sequence and the classified motifs of CAPE1 proprotein (Tomato PR-1b) (SEQ ID NO: 57). (b) Phylogenetic analysis of 17 selected CAPE proproteins generated by MEGA5.2 using the Maximum Likelihood method based on the Whelan and Goldman model. Bootstrap values set to 1,000 replicates. (c) The sequence identities and logo illustration of 30CAPE1 homologs generated by Weblogo (http://weblogo.berkeley.edu/logo.cgi). SP: Signal Peptide, CAP Domain: cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins domain.

FIG. 9 shows identification of CAPE homologs in Arabidopsis and the anti-pathogen activity of AtCAPE1 (SEQ ID NO: 19) and AtCAPE9. (a) The putative AtCAPE peptides derived from the CAP proteins in Arabidopsis containing a conserved cleavage (CNYx) (SEQ ID NO: 55) and a signaling peptide (PxGNxxxxxPY) motif (SEQ ID NO: 28). According to their identities, the highest identity of CAPE is derived from At4g33730, designated AtCAPE1; the lowest identity of CAPE is derived from At2g14610 (PR1), designated AtCAPE9. Red characters indicated different amino acids compared to SolCAPE1 (b) The Pst DC3000 infection phenotypes for the plants presprayed with water, 100 nM AtCAPE1, AtCAPE9 or 100 nM flg22 peptide for 2 hours (n=3) prior to pathogen inoculation. The infection symptoms were observed 4 days after inoculation. The bacterial numbers were calculated 4 days after inoculation and are represented as log colony-forming units (Log CFU) per g leaf tissue. Data represent the means and SD of three biological samples. A statistically significant difference compared with the corresponding water-treated samples is indicated with ** (P<0.01) or *** (P<0.001) based on Student's t-test.

FIG. 10 shows the AtCAPE1 production can be induced by salt in Arabidopsis. (a) Production of the precursor PROAtCAPE1 and the AtCAPE1 peptide was cleaved from PROAtCAPE1 in CAPE1oxCNYD without (−) or with different NaCl concentration for 24 hours. The putative CAPE is shown in red. The numbers indicate the predicted molecular weight of precursor protein tagged with eYFP (45.7 kDa) and the cleaved precursor tagged with eYFP (26.3 kDa). (b) Protein extracts from the transgenic lines (CAPE1oxCNYD) harbouring the AtCAPE1-eYFP fusion grown with (+) and without (−) 125 mM NaCl for the indicated times were subjected to western blot analysis. The upper and lower bands with approximate size of 45.7 KDa and 26.3 KDa represent the expected size of the PROAtCAPE1-eYFP fusion protein and the AtCAPE1-eYFP fusion protein, respectively. The fusion proteins were detected by anti-GFP antibody. α-tubulin, loading control. (c) Relative level of endogenous AtCAPE1 in shoots and roots. Seedlings grown for 24 h without (½ MS) and with 125 mM NaCl were subjected to quantitative LC-MS/MS analysis. IS, internal standard. The average values from two biological repeats are shown. Error bars, means±SE. Asterisks indicate statistically significant differences between salt treated and untreated samples (Student's t-test; **P<0.01).

FIG. 11 shows salt treatment can induce AtCAPEs for enhancing plant immune responses in Arabidopsis. 5 days Arabidopsis seedlings treated with 50 mM NaCl for 24 hours and following the treatment of with or without 250 nM AtCAPE1 for 6 hours. The infection symptoms were observed 4 days after Pst DC3000 inoculation. The bacterial numbers were calculated 7 days after inoculation and represented as log colony-forming units (Log CFU) per g leaf tissue. Data represent the means and SD of three biological samples.

FIG. 12 shows the production of the precursor PROAtCAPE1 and the cleaved PROAtCAPE1 in CAPE1oxCNYD and CAPE1oxCNAD transgenic plants, where eYFP was fused to PROAtCAPE1 containing wild type (CNYD, SEQ ID NO: 61) and the mutated (CNAD, SEQ ID NO: 62) junction sequence, respectively. T3 seedlings derived from independent transgenic lines were sampled for western blotting with anti-GFP antibody. Coomassie blue staining was used for protein loading control.

FIG. 13 shows the cleavage motif (CNYX.) of PR-1b inhibited defense gene expression in tomato. Relative expression levels of PR-1b and WRKY53 were analyzed by qRT-PCR 2 h after challenge of 10⁷ cfu/mL Pst DC3000 hrcC⁻ or buffer in tomato leaves, which was pretreated with water, 100 nM CAPE1 or 1 μM CNYDPV for 2 h, respectively.

DETAILED DESCRIPTION OF THE INVENTION

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by a person skilled in the art to which this invention belongs.

As used herein, the singular forms “a”, “an”, and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a component” includes a plurality of such components and equivalents thereof known to those skilled in the art.

The term “comprise” or “comprising” is generally used in the sense of include/including which means permitting the presence of one or more features, ingredients or components. The term “comprise” or “comprising” encompasses the term “consists” or “consisting of.”

The terms “polypeptide” and “peptide” as used herein are interchangeable. As used herein, the term “defense signaling peptide/polypeptide” refers to a peptide or a polypeptide of about 10 or more amino acid residues in length that has substantial defense signaling peptide activity e.g. activation of anti-herbivore or anti pathogen genes or induction of plant hormones to enhance immune activities. Preferably, defense signaling peptides or polypeptides up to about 150 amino acid residues or 100, or 90, or 80, or 70, or 60, or 50, or 40, or 30, or 20, or 15 amino acid residues are included in the defense signaling peptides or polypeptides as described herein.

In this study, an MS-based peptidomics approach using a hypothetical peptide database combining a target-decoy search strategy and differential database match scoring is developed to discover defense signaling peptides. This platform is demonstrated by the identification of defense peptides induced by wounding plus methyl jasmonate (MeJA) treatment in Solanum lycopersicum (tomato). Using this platform, several peptides including systemin have been identified and quantified to be wounding- plus MeJA-induced. One of the peptides induced by wounding only or wounding plus MeJA is found to activate immune signals for defense against biological threats.

Accordingly, the present invention provides an isolated peptide having a conserved motif of SEQ ID NO: 1 (PxGNxxxxxPY) which can act as a defense signaling peptide. The present invention provides also provides an isolated peptide having a conserved motif of SEQ ID NO: 28 (CNYxPxGNxxxxxPY) which can also be applied to plants where a specific cleavage by a proteolytic enzyme can occur such that the defense signaling peptide having SEQ ID NO: 1 is generated to provide a desired defense activity in the plants. See Table 1.

TABLE 1 Motif SEQ ID NO PxGNxxxxxPY  1 CNYxPxGNxxxxxPY 28

In some embodiments, the plant defense signaling peptide as described herein is selected from the group consisting of SEQ ID NO: 2-27 or SEQ ID NO: 29-54. Sec Table 2.

TABLE 2 Accession SEQ ID Plant species no. Sequence NO S. lycopersicum P04284(PR1b)      PVGNWIGQRPY  2 CNYD PVGNWIGQRPY 29 S. lycopersicum Q04108      PVGNWVGERPY  3 CNYD PVGNWVGERPY 30 C. annuum AAX20041      PVGNWVGQRPY  4 CNYD PVGNWVGQRPY 31 C. frutescens AAQ19681      PVGNWVGQRPY  5 CNYD PVGNWVGQRPY 32 S. tuberosum AAL01594      PVGNWVGORPY  6 CNYD PVGNWVGQRPY 33 S. phrueja CAD38276      PVGNYVGQRPY  7 CNYD PVGNYVGQRPY 34 N. glutinosa AAB05225      PPGNFVGQSPY  8 CNYD PPGNFVGQSPY 35 N. tabacum P07053      PPGNVIGQSPY  9 CNYD PPGNVIGQSPY 36 V. vinifera XP_002274371      PPGNYVGQRPY 10 CNYD PPGNYVGQRPY 37 V. hybrid ADN43417      PPGNYVGQRPY 11 cyltivar CNYD PPGNYVGQRPY 38 V. ADN43428      PPGNYVGQRPY 12 shuttleworthii CNYD PPGNYVGQRPY 39 B. napus AAB06458      PRGNYVNEKPY 13 CNYD PRGNYVNEKPY 40 B. rapa AAT46023      PRGNYVNEKPY 14 CNYD PRGNYVNEKPY 41 G. max XP_003545770      PPGNYVGQRPY 15 CNYA PPGNYVGQRPY 42 M. truncatula AFK38989      PPGNYVGQKPY 16 CNYD PPGNYVGQKPY 43 Z. mays DAA59477      PPGNFRGQRPY 17 CNYN PPGNFRGQRPY 44 O. sativa EE54618      PRGNIVGRRPY 18 CNYE PRGNIVGRRPY 45 Arabidopsis AT4G33730.1      PAGNYIGARPY 19 CNYD PAGNYIGARPY 46 Arabidopsis AT4G25780.1      PPGNYIGQKPY 20 CNYD PPGNYIGQKPY 47 Arabidopsis AT4G33720.1      PPGNWVGEWPY 21 CNYD PPGNWVGEWPY 48 Arabidopsis AT4G25790.1      PPGNYVGEKPY 22 CNYD PPGNYVGEKPY 49 Arabidopsis AT5G57625.1      PPGNYVGEKPY 23 CNYD PPGNYVGEKPY 50 Arabidopsis AT4G30320.1      PPGNFLGRKPY 24 CNYD PPGNFLGRKPY 51 Arabidopsis AT2G14580.1      PPGNYANQKPY 25 (PRB1) CNYD PPGNYANQKPY 52 Arabidopsis AT5G26130.1      PPGNYRGRWPY 26 CNYY PPGNYRGRWPY 53 Arabidopsis ATG14610.1      PRGNYVNEKPY 27 (PR1) CNYD PRGNYVNEKPY 54

A plant defense signaling peptide as described herein may be produced chemical synthesis using techniques well known in the chemistry of proteins such as solid phase synthesis or synthesis in homogenous solution.

Alternatively, the peptide of the present invention may be prepared using recombinant techniques. In this regard, a recombinant nucleic acid comprising a nucleotide sequence encoding a polypeptide of the present invention and host cells comprising such recombinant nucleic acid are provided. The host cells may be cultured under suitable conditions for expression of the polypeptide of interest. Expression of the polypeptides may be constitutive such that they are continually produced or inducible, requiring a stimulus to initiate expression. In the case of inducible expression, protein production can be initiated when desired by, for example, addition of an inducer substance to the culture medium, for example, isopropyl □-D-1-thiogalactopyranoside (IPTG) or methanol. Polypeptide can be recovered and purified from host cells by a number of techniques known in the art, for example, chromatography e.g., HPLC or affinity columns.

In some embodiments, the peptide of the present invention can be said to be “isolated” or “purified” if it is substantially free of cellular material or chemical precursors or other chemicals that may be involved in the process of peptide preparation. It is understood that the term “isolated” or “purified” does not necessarily reflect the extent to which the peptide has been “absolutely” isolated or purified e.g. by removing all other substances (e.g., impurities or cellular components). In some cases, for example, an isolated or purified peptide includes a preparation containing the peptide having less than 50%, 40%, 30%, 20% or 10% (by weight) of other proteins (e.g. cellular proteins), having less than 50%, 40%, 30%, 20% or 10% (by volume) of culture medium, or having less than 50%, 40%, 30%, 20% or 10% (by weight) of chemical precursors or other chemicals involved in synthesis procedures.

In use, the defense signaling peptide of the invention can be admixed with an agriculturally acceptable carrier to form an agricultural composition which is to be applied to plants in need. Examples of the agriculturally acceptable carrier as used in the invention include but are not limited to water, alcohols, mineral or vegetable oils, calcium carbonate, talc, powdered magnesia, gypsum, and diatomaceous earth. The agricultural composition may be in the form of emulsions, liquids, oils, water soluble powders, wettable powders, flowables, powders, subtilized granules, granules, aerosols, fumigants, pastes and the like.

According to the present invention, the defense signaling peptide of the invention or a composition comprising the same can be applied to a plant to increase plant defense activity. It is effective in inducing systemic immune responses so as to increase resistance against biological threats.

Specifically, the plant applied with the defense signaling peptide of the invention or a composition comprising the same exhibit increased defense activity, as compared to a control plant without application of the defense signaling peptide of the invention or a composition comprising the same.

In certain embodiments, the defense activity as described herein includes production of hydrogen peroxide (H₂O₂), generation of a plant hormone, e.g. jasmonate (JA), JA conjugated with amino acid isoleucine (JA-Ile) or salicylic acid (SA), or expression of an anti-herbivore or anti-pathogen protein, e.g. proteinase inhibitor 1 (PI-1), proteinase inhibitor 2 (PI-2), pathogenesis-related protein 1b (PR-1b, cape1 precursor gene), beta-1,3-glucanase (PR-2), cys protease (PR-7), class ii chitinase (Chi2;1), ethylene response factor 5 (ERF5) or avrpto-dependent pto-interacting protein 3 (Adi3). See FIG. 3.

In particular, the present invention is useful in increasing a plant's resistance to a wide variety of pathogens, including but not limited to, bacteria, insects, nematodes, fungi and the like.

In certain embodiments, insect larvae fed with plant leaves pre-treated with a defense signaling peptide of the invention exhibit a reduced size by about 20%, as compared with control insect larvae fed with plant leaves pre-treated with water. See FIG. 4 (a).

In certain embodiments, a plant pre-sprayed with a defense signaling peptide of the invention exhibits reduced infection symptoms and decreased bacterial numbers per fresh weight, after bacterial inoculation, as compared with a control plant without application of the defense signaling peptide of the invention. See FIG. 4(b).

The defense signaling peptide of the invention is applicable to a verity of plant species. Plants to which the inventive method can be applied include both monocotyledon and dicotyledon. Examples of monocotyledon includes but not limited to rice, barley, wheat, rye, oat, corn, bamboo, sugar cane, onion, leek and ginger. Examples of the dicotyledons include, but are not limited to Arabidopsis thaliana, eggplant, tobacco plant, red pepper, tomato, burdock, crown daisy, lettuce, balloon flower, spinach, chard, potato, celery, carrot, water dropwort, parsley, Chinese cabbage, cabbage, radish, watermelon, melon, cucumber, pumpkin, gourd, strawberry, soybean, mung bean, kidney bean, and pea.

In some embodiments, a defense signaling peptide as described herein is included in a composition at a concentration of about 50 nM or more, 100 nM or more, 150 nM or more, 200 nM or more or 250 nM or more.

In some embodiments, a composition comprising a defense signaling peptide as described herein is sprayed to a plant in need for 1 min or more and the defense response can be induced within 2 hours and last more than 24 hours.

Accordingly, the method of the invention for treating a plant to increase plant defense activity by using a defense signaling peptide as described herein provides a variety of advantages, at least including (1) it is effective in inducing systemic immune responses in plants against numerous biological threats; (2) it is performed by simply applying the defense signaling peptide of the invention to a plant in need, (3) a low dose of the defense signaling peptide of the invention is sufficient; (4) the defense signaling peptide of the invention is short in length and can be easily made by chemical synthesis; and (5) no transgenic technology or agrichemicals is needed which may cause environmental problems.

In some embodiments, an overly strong defense activity in plants is not preferred due to decreased growth. Therefore, proper regulation of a defense activity is desired. In the present invention, it is found that the CNYx (SEQ ID NO: 55) is a core structure for designing protease inhibitor to prevent processing and decrease defense activity. Therefore, a peptide having the CNYx motif (SEQ ID NO: 55) but lacking the active PxGNxxxxxPY motif (SEQ ID NO: 1) to provide a define activity can be used as a protease inhibitor/competitor to reduce or block activity of the endogenous protease in cleaving the precursor peptide to generate the active defense signaling peptide of PxGNxxxxxPY (SEQ ID NO: 1) and thus to regulate the defense activity in plants.

Accordingly, the present invention relates to a method of down regulating a defense activity in a plant, comprising treating the plant with a peptide having a CNYx motif (SEQ ID NO: 54) but lacking a 11-amino acid signaling peptide motif (PxGNxxxxxPY) (SEQ ID NO: 1) in an amount to effectively reduce or block the enzymatic activity in cleaving a precursor peptide (e.g. CNYxPxGNxxxxxPY (SEQ ID NO: 15) or the full length of PR-1) to generate a plant defense signaling peptide of PxGNxxxxxPY (SEQ ID NO: 1) as described above.

In some embodiments, a peptide as a protease inhibitor according to the present invention preferably has up to about 50 amino acid residues or 40, or 30, or 20, 15 or 10 amino acid residues, for example, at least 4 amino acid residues, particularly 5, 6, 7, 8, 9 or 10 amino acid residues. In a specific example, a peptide as a protease inhibitor according to the present invention is SEQ ID NO: 55 (CNYDPV).

The present invention is further illustrated by the following examples, which are provided for the purpose of demonstration rather than limitation. Those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.

Examples

Many important intercellular communication events in multicellular organisms are mediated by peptides, but only a few peptides have been identified in plants. In an attempt to address the difficulties in identifying plant signaling peptides, we developed a novel peptidomics approach and used this approach to discover defense signaling peptides in plants. In addition to the canonical peptide systemin, several novel peptides were confidently identified in Solanum lycopersicum (tomato) and quantified to be both wounding- and MeJA-induced. A wounding or wounding plus MeJA-induced peptide derived from the pathogenesis-related protein 1 (PR-1) family was found to induce significant anti-pathogen and minor anti-herbivore responses in tomato. This study highlights a role for PR-1 in immune signaling and suggests the potential application of plant endogenous peptides in efforts to defeat biological threats in crop production. As PR-1 is highly conserved across many organisms and the putative peptide from At-PR1 was also found to be bioactive in Arabidopsis, our results suggest that this peptide may be useful for enhancing resistance to stress in other plant species.

1. Material and Methods

1.1 Chemicals, Enzymes and Materials

Tris (2-carboxyethyl) phosphine hydrochloride (TCEP), methyl methanethiosulfonate (MMTS), 3,3-diaminobenzidine (DAB), potassium hydroxide (KOH), sodium hydroxide (NaOH), hydrogen chloride (HCl), 10× Murashige and Skoog (MS) basal salt micronutrient mixture, King Agar B medium, isopropanol, ethanol, chloroform, methyl jasmonate (MeJA, 95% solution), Triton X-100, β-casein, salicylic acid (SA), 2-hydroxybenzoic acid-[²H₆] (d₆-SA) and jasmonic acid (JA) were purchased from Sigma-Aldrich (St. Louis, Mo.). Dihydrojasmonic acid (H₂JA) was purchased from OlChemim (Olomouc, Czech Republic). Analytical grade methanol, acetonitrile (ACN) and trifluoroacetic acid (TFA) were purchased from Merck (Darmstadt, Germany). LC-MS grade ACN with 0.1% formic acid (FA) was from J. T. Baker (Phillipsburg, N.J.). Deionized water (18.1 MΩ·cm resistivity) from Milli-Q system (Millipore, Bedford, Mass.) was used throughout this work. C18 Zip Tip and Millex HA 0.45 μm filters were purchased from Millipore (Billerica, Mass.). The TriPure RNA Isolation Reagent and FastStart Universal SYBR Green Master (ROX) Kit were purchased from Roche (Indianapolis, Ind.). The RNA purification reagent RNAmate was from BioChain (Hayward, Calif.). The SuperScript III Reverse Transcriptase Kit was purchased from Invitrogen (Carlsbad, Calif.). Fast-Run HotStart PCR Mix was from Postech (Taipei, Taiwan). Miracloth was purchased from Calbiochem (La Jolla, Calif.). The customized Sep-Pak C18 Cartridge 60 cc (20 g) was purchased from Waters (Wexford, Ireland). Gel filtration XK 16/40 column and packing gel (Sephadex G-25 Fine) were purchased from GE Healthcare Bio-Sciences AB (Uppsala, Sweden). Tryptic enolase and [Glu1]-Fibrinopeptide (GFP) was purchased from Waters (Milford, Mass.). Trypsin (modified, sequencing grade) was purchased from Promega (Madison, Wis.). Systemin (AVQSKPPSKRDPPKMQTD, SEQ ID NO: 58), CAPE1 (PVGNWIGQRPY, SEQ ID NO: 2), AtCAPE1 (PAGNYIGARPY, SEQ ID NO: 19) AtCAPE9 (PRGNYVNEKPY, SEQ ID NO: 27), cleavage motif (CNYDPV, SEQ ID NO: 56) and internal standard (PAAAYIGARAY, SEQ ID NO: 59) were synthesized and purified to >95% purity by Yao-Hong Biotechnology (Taipei, Taiwan). The flg22 (QRLSTGSRINSAKDDAAGLQIA, SEQ ID NO: 60) with purity >95% purity was purchased from KareBay Biochem, Inc. (Monmouth Junction, N.J.). The purity of synthetic peptide was further checked to over 95% using nanoUHPLC-MS.

1.2 Plant Materials and Growth Conditions

Tomato (Solanum lycopersicum cv. CL5915) seeds were provided by AVRDC—The World Vegetable Center (Tainan, Taiwan). The tomato plants were kept at 25° C. day/20° C. night temperature under a 12 hour light/12 hour dark photoperiod. Tomato seeds were germinated in soil and grown in a growth chamber for 2 weeks. For detection of endogenous peptides, the 2-week-old plants were transferred and maintained in a phytotron for 6 weeks. The tomato plants for peptide treatments were continuously grown in a growth chamber for 5 weeks. To examine the peptide activity in Arabidopsis. Arabidopsis thaliana (ecotype Columbia) seeds were germinated in soil and grown in a growth chamber at 22° C. day/20° C. night temperature under a 8 hour light/16 hour dark photoperiod for 4 weeks. For salt treatment. Seeds were surface sterilized with 30% bleach (CLOROX) for 8 min and then washed with sterilized ddH2O five times. Seeds were germinated on half-strength Murashige and Skoog (½ MS) medium under a 16 h photoperiod (80-100 μmol m⁻2 s⁻1 illumination) at 22° C.

1.3 Plant Treatments

To extract the wound-induced peptides, the tomato plants were mechanically wounded by cutting across the surface of the mesophyll with a pair of scissors and spraying with 1.25 mM MeJA in 0.1% Triton X-100 solution for 15 hours (Pearce et al., 2001a). For direct quantitation of CAPE1 in tomato, unwounded, wounded, or wounded plus MeJA treated plants for 15 hours were used to study peptide induction. To examine the possible function of peptide using cDNA microarray analysis, detached tomato leaves were immersed in water or 250 nM CAPE1 in aqueous solution for 1, 2, 4, and 8 hours, respectively. To confirm the gene expression induced by the peptide, the tomato plants were collected after spraying with 250 nM CAPE1 or water for 0, 4, 8 and 24 hours. To compare the ROS induced by different treatments, detached tomato leaves were treated with water (control), mechanical wounding (MW), 1.25 mM MeJA, 250 nM systemin or 250 nM CAPE1 for 4 hours. To test the anti-herbivore activity induced by the peptide, the tomato plants were collected after spraying with 250 nM CAPE1 or water for 24 hours before feeding with insects. To compare the PI genes induced by the peptides, detached tomato leaves were immersed in 250 nM CAPE1, 250 nM systemin or water for 1, 2, and 4 hours. To compare the jasmonates induced by the peptides, the excised tomato plants were treated with 10 mM phosphate buffer, 365 nM systemin or 365 nM CAPE1 in buffer through the cut stem for 2 and 4 hours (Schaller et al., 1995; Howe et al., 1996). To compare the salicylic acid induced by peptides, the tomato plants were treated with 10 mM phosphate buffer, 365 nM flg22 or 365 nM CAPE1 in buffer through the cut stems of excised plants for 8 hours. To compare the WRKY53 and PR-1b genes induced by the peptides, detached tomato leaves were immersed in 250 nM CAPE1, 250 nM flg22 or water for 2 hours. To test the anti-pathogen activity induced by peptides, three groups of the tomato plants were sprayed with 100 nM CAPE1, 100 nM flg22, or water, respectively, for 2 hours prior to pathogen challenge. To test the anti-pathogen activity induced by peptides in Arabidopsis, the plants were sprayed with 100 nM AtCAPE1, AtCAPE9, 100 nM flg22 or water, respectively, for 2 hours prior to pathogen challenge. Arabidopsis seedlings treated with 50 mM NaCl for 24 h with or W/O 250 nM AtCAPE1 or AtCAPE9 for 6 h after salt treatment. To test cleavage motif can be a protease inhibitor, the tomato plants were sprayed with 1 M CNYDPV for 2 hours prior to pathogen challenge.

1.4 Endogenous Peptide Extraction in Tomato and Arabidopsis

The unwounded and wounding plus MeJA treated tomato leaves were collected and individually ground into powder under liquid nitrogen by a blender (Waring Commercial, New Hartford, N.Y.). Frozen leaf powder (150 g) was dissolved in 200 ml of 1% TFA and homogenized to leaf juice by a blender for 2 minutes. The leaf juice was filtered through four layers of cheesecloth and one layer of Miracloth. The filtrated leaf juice was then centrifuged at 10,000×g for 20 minutes at 4° C. The supernatant was adjusted to pH 4.5 with 10 N NaOH and centrifuged at 10,000×g for 20 minutes at 4° C. Then the supernatant was re-adjusted to pH 2.5 using TFA and 150 μg tryptic β-casein peptides were added to the supernatant as an internal control for peptide quantity before purification. To avoid the trypsin residue reacting with the endogenous proteins or peptides, the tryptic β-casein peptides were acidified by TFA and purified using C18 Zip Tip. Before purifying the supernatant using a Sep-Pak cartridge, the stationary phase was first equilibrated by 60 ml 0.1% TFA. The supernatant was loaded into the Sep-Pak cartridge, washed with 120 ml 0.1% TFA and eluted by 200 ml of 60% methanol in 0.1% TFA. The eluted solution was vacuum-evaporated to remove methanol using a vacuum centrifugation concentrator (miVac Duo Concentrator, Genevac, Gardiner, N.Y.) first and then using a lyophilizer (EYELA, Miyagi, Japan) to dryness (Pearce et al., 1991). To profile total endogenous peptides using LC-MS operated in data dependent acquisition (DDA) mode, the lyophilized crude extract was dissolved in 1 ml of 0.1% TFA, centrifuged at 10,000×g for 10 minutes at 4° C. and filtered through a Millex HA 0.45 μm filter before peptide fractionation. For the peptide fractionation, the filtrated peptide extract was injected into a Sephadex G-25 column and eluted by 1 ml/min of 0.1% TFA with 1 fraction/min collection. Ten fractions from elution times of 22-31 minutes were collected and evaporated to dryness using a vacuum centrifugation concentrator. Each fraction was purified by C₁₈ Zip Tip for LC-MS/MS analysis. For targeted peptide analysis using LC-MS operated in selected reaction monitoring (SRM) mode, the endogenous peptides were extracted from the unwounded, wounding only and wounding plus MeJA treated tomato leaves using the same procedure but without gel-filtration fractionation. Ten-day-old Arabidopsis seedlings grown vertically on ½ MS medium were transferred to a hydroponic system culture of ½ MS liquid medium without sucrose. The medium was changed every 4 days. Three weeks after planting, the plant tissue was harvested. For salt treatments, fresh ½ MS medium in the presence or absence of 125 mM NaCl was exchanged and the treatments were prolonged to 24 h. Samples were homogenized with 200 ml of 1% (v/v) chilled trifluoroacetic acid (TFA; Sigma-Aldrich) in a blender for 2 min. To normalize the variations in sample preparation and for better quantification accuracy by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis, 20 μl of 1 pmole μl-1 of internal standard (synthetic peptide: PAAAYIGARAY, SEQ ID NO: 59) with two amino acid substitutions of G3A and N4A of AtCAPE1 was added to the extraction buffer while crude peptide was isolated. The extracts were then filtered through four layers of Miracloth (Calbiochem, San Diego, Calif., USA) to remove plant debris. The procedure followed a previously described protocol (Pearce et al., 2001a, b). After centrifuging at 8500 rpm for 20 min at 4° C. (Beckman Coulter, Avanti J-26 XP), the pH value of the supernatant was adjusted to 4.5. The extracts were then centrifuged again at 8500 rpm for 20 min at 4° C. and the pH value of supernatant was adjusted to 2.5. Subsequently, the supernatant was bound with a customized Sep-Pak C18 solid phase extraction cartridge (Waters, Milford, Mass., USA) according to the following steps: the C18 cartridge was conditioned by 0.1% (v/v) TFA first, bound with the supernatant, and then washed with 0.1% (v/v) TFA. Finally, the polypeptides were eluted with 60% (v/v) methanol/0.1% (v/v) TFA. The peptides in the final eluate were evaporated to dryness by rotary evaporation under high vacuum, and the pellets were resuspended in 0.1% (v/v) TFA. The polypeptides were further fractionated by fast protein liquid chromatography (ÄKTA purifier) to remove protein contaminates with size exclusion columns (Superdex peptide 10/300 GL; GE Healthcare, Little Chalfont, UK). Fractions containing polypeptides or small proteins with similar sizes to AtCAPE1 were collected and combined. The combined eluates were rotary evaporated under high vacuum and resuspended in 0.1% (v/v) TFA for ZipTip (Millipore, Billerica, Mass., USA) to remove the contamination of salts. After final evaporation and resuspension in 0.1% (v/v) formic acid (Fluka), targeted LC-MS/MS analysis was performed. Targeted LC-MS/MS analysis.

1.5 Endogenous Peptide Profiling Using LC-MS/MS

For endogenous peptide profiling, LC-MS/MS analysis was performed with a nanoUHPLC system (nanoACQUITY UPLC, Waters, Millford, Mass.) coupled online to the nano-electrospray source of a hybrid quadruple time-of-flight mass spectrometer (SYNAPT HDMS G1, Waters, Manchester, UK). The SYNAPT HDMS G1 instrument was operated in the positive ion mode and DDA methods for detection of endogenous peptides. The sample was loaded into a 180 μm×50 mm tunnel frit trap column packed with 20 mm of 5 μm Symmetry C18 particles (Waters, Millford, Mass.) and separated online with a 75 μm×250 mm tunnel fit analytical column packed with 250 mm of 1.7 μm BEH C18 particles (Waters, Millford, Mass.) using a 95 minute gradient flow with 300 nl/min and 5-90% ACN/0.1% FA ratio (Chen et al., 2012). The DDA acquisition parameters were set to one full MS scan (m/z 400-1600) with a scan time of 0.6 seconds and switched to three product ion scans (m/z 100-1990) with a scan time of 1.2 seconds when a precursor ion charge was 2+, 3+ and 4+ and an intensity greater than 20 counts was detected. The data generated from SYNAPT HDMS G1 were first converted into mzXML format (Pedrioli et al., 2004) using massWolf (version 4.3.1) and then processed by UniQua with default parameters for SYNAPT HDMS G1 (Chang et al., 2013). The UniQua processed spectra were converted into Mascot generic format (.mgf) using mzXML2Search from Trans Proteomics Pipeline (TPP) version 4.4 rev. 1 (Pedrioli, 2010). For detection of Arabidopsis CAPE1, an LTQ Velos PRO mass spectrometer (Thermo Scientific, Waltham, Mass., USA) coupled with an online capillary nanoUHPLC system (Waters) was utilized for peptide identification and quantification. The capillary LC system was equipped with a homemade C18 trap cartridge (5 μm particles, Symmetry C18; Waters), and a homemade C18 reversed-phase analytical column (1.7 μm particles, BEH130 C18; Waters) (Chen et al., 2012) was used to deliver the solvent and target peptide with a linear gradient from 8 to 90% (v/v) acetonitrile in 0.1% (v/v) formic acid for 95 min at a nanoflow rate (approx. 300 nl min-1). The analytical column was coupled to a nanoelectrospray ionization source, and acquisition of the data was performed with a full MS scan followed by MS/MS scans of the targeted precursor ions. Precursor ions of AtCAPE1 (PAGNYIGARPY (SEQ ID NO: 19); m/z 589.8) and the internal standard (PAAAYIGARAY (SEQ ID NO: 59); m/z 562.4) were selected for subsequent targeted MS/MS scans. The fragment ions m/z 563.2, 676.3, and 900.5 and m/z 537.2, 650.3, and 813.34 were used for further identification and quantification of AtCAPE1 and the internal standard, respectively.

1.6 Hypothetical and Decoy Database

The tomato hypothetical peptide database (TomHT database) was composed by extracting 50 residues of all protein C-terminal sequences from the International Tomato Annotation Group (ITAG) protein database (release version 2.3, total protein entries=34,728) with the addition of the bovine β-casein sequence. The randomized databases (Ran Databases) were generated by shuffling sequences in the target databases using Perl script (decoy.pl) provided by Matrix Science (London, UK).

1.7 Endogenous Peptide Identification and Quantitation

The processed mgf files were searched against the TomHT database without specifying enzyme cleavage rules using a Mascot MS/MS ion search (Matrix Science, server version 2.3). The mass tolerance in the MS/MS ion search for peptide precursors and fragments was ±0.1 Da. The Mascot search results from the randomized database were used to evaluate the score to cutoff the random matched peptides.

1.8 Phytohormone Extraction

After peptide treatment, the metabolites were extracted from leaf tissues for phytohormone quantitation. The extraction procedure was modified from a previously published protocol (Pan et al., 2010). The leaf tissues (about 0.6 g fresh weight) were ground into powder under liquid nitrogen and transferred to a 50 ml screw-cap tube. The frozen leaf powder was dissolved in 6 ml extraction solvent and d6-SA (3 ng to 0.6 g leaf tissue) and H₂JA (15 ng to 0.6 g leaf tissue) were added as internal standards. The samples were extracted by shaking at a speed of 100 rpm at 4° C. for 30 minutes and then 12 ml dichloromethane was added to each sample and shaken at 100 rpm at 4° C. for 30 minutes. The samples were centrifuged at 13,000×g at 4° C. for 5 minutes, and two phases were formed. The lower phase was transferred carefully into a new tube and evaporated to dryness by a vacuum centrifugal concentrator for about 1 hour. The dried samples were dissolved in 300 μl methanol, mixed well and centrifuged at 10,000×g at 4° C. for 5 minutes and then the supernatant was transferred to the sample vial for targeted quantitation analysis using LC-MS/MS.

1.9 Targeted Peptide and Phytohormone Quantitation Using LC-MS/MS

For targeted peptide quantitation, the nanoUHPLC method was the same as for endogenous peptide profiling and the MS (LTQ Velos Pro, Thermo Fisher Scientific, San Jose, Calif.) was set to one full MS scan (m/z 400-1600) with enhanced scan speed and switched to one selected reaction monitoring (SRM) scan with normal scan speed. For SRM targeted on CAPE1, the doubly charged CAPE1 precursor ion m/z was selected (m/z 643.84) for fragmentation and product ions m/z of 620.34, 733.37 and 1090.57 were monitored. The relative abundances of CAPE1 in wounded and unwounded samples were estimated by combining SRM peak areas of product ions.

For phytohormone quantitation, a linear ion trap-orbitrap mass spectrometer (Orbitrap Elite, Thermo Fisher Scientific, Bremen, Germany) coupled online with a UIIPLC system (ACQUITY UPLC, Waters, Millford, Mass.) was used. The phytohormones were separated by a HSS T3 column (Waters, Millford, Mass.) using gradients of 0.5-25% ACN at 0-2 min, 25-75% ACN at 2-7 minutes and 75-9.5% ACN at 7-7.5 minutes. The mass spectrometer was operated in the negative ion mode and set to one full FT-MS scan (m/z 100-600) with 60,000 resolution and switched to five FT-MS product ion scans (in 30,000 resolution) for five precursors: m/z of 137.02 (for SA), 209.12 (for JA), 322.20 (for JA-Ile), 141.05 (for d₆-SA dissociated to d₄-SA) and 211.13 (for H₂JA). The fragmentation reactions of m/z 137.02 to 93.03 for SA, 209.12 to 59.01 for JA, 322.20 to 130.09 for JA-Ile, 141.05 to 97.06 for d₆-SA and 211.13 to 59.01 for H₂JA were selected for quantitation. The absolute abundances of JA, JA-Ile and SA were calculated by the abundance of d₆-SA and H₂JA.

1.10 Quantitative Real Time PCR (qRT-PCR)

Quantitative real-time PCR (qRT-PCR) was used to validate the expression of some specific genes. Three biological replicates were used for qRT-PCR analyses. The qRT-PCR was performed using SYBR Green reagent and ABI 7500 Real Time PCR systems (Foster City, Calif.). The PCR cycling steps were 50° C. for 2 min and 94° C. for 10 min for initial steps and followed by 95° C. for 15 s and 60° C. for 1 min for 40 cycles. The gene expressions across different samples were normalized with internal control EF-1α or Ubi3. The primers used are listed in Table 3. The melting curve was used to verify the specificity of the PCR product.

TABLE 3 primers for qRT-PCR. Product Gene size Gene Accession # Primer (5′->3′) (bp) Elongation Factor 1α X14449 For: CTCCGTCTTCCACTTCAGG 128 (EF-1α) (SEQ ID NO: 63) Rev: TCAGTTGTCAAACCAGTAGGG (SEQ ID NO: 64) Ubiquitin 3 X58523 For: ACTCTTGCCGACTACAACATCC 198 (Ubi3) (SEQ ID NO: 65) Rev: CTCCTTACGAAGCCTCTGAACC (SEQ ID NO: 66) Proteinase Inhibitor K03290 For: CTTCTTCCAACTTCCTTTG 110 1 (PI-1) (SEQ ID NO: 67) Rev: TGTTTTCCTTCGCACATC (SEQ ID NO: 68) Proteinase Inhibitor K03291 For: AATTATCCATCATGGCTGTTCAC 254 2 (PI-2) (SEQ ID NO: 69) Rev: CCTTTTTGGATCAGATTCTCCTT (SEQ ID NO: 70) AvrPto-dependent NM_001247682 For: AGGCAGTTTCCTATAGGGGCTA 155 Pto-interacting (SEQ ID NO: 71) protein 3 Rev: TCGACCATCAGGTCTTCTTCC (Adi3) (SEQ ID NO: 72) Ethylene response NM_001247583 For: ATGGGTTCTCCACAAGAGAC 132 factor 5 (SEQ ID NO: 73) (ERF5) Rev: GAAGCTTGCGATGTCATCAA (SEQ ID NO: 74) Pahtogenesis-related M69248.1 For: CTCATATGAGACGTCGAGAAG 204 protein 1b (SEQ ID NO: 75) (PR-1b) Rev: GGAAACAAGAAGATGCAGTACTTAA (SEQ ID NO: 76) beta-1,3-glucanase NM_001247869.1 For: CAAATAACAGGAGCGCAGCC 163 (PR-2) (SEQ ID NO: 77) Rev: GTTACTTCCTTTGAGGGCAT (SEQ ID NO: 78) Cys protease CK574973.1 For: TCAGCACCTCTGGACCTTT 141 (PR-7) (SEQ ID NO: 79) Rev: GCTCCTGAAGGCTCTGTTA (SEQ ID NO: 80) Class II chitinase U30465.1 For: TTTTGGTCGAGGTCCTATCC 186 (Chi; 2) (SEQ ID NO: 81) Rev: GTAATGACATCGTGTGCCGA (SEQ ID NO: 82) WRKY transcription Solyc08g008280.2.1 For: AAATGGATTGTGCATCAAACTGGGA 189 factor 53 (WRKY53) (SEQ ID NO: 83) Rev: AGCCACCCCAGTTGAGAATCAACA (SEQ ID NO: 84)

1.11 In Vivo Detection of H₂O₂

The 3,3-diaminobenzidine (DAB) was dissolved with 1 N HCl and adjusted to pH 3.8 with NaOH to a final concentration of 1 mg/ml. After plant treatments, the detached leaves were continuously supplied with DAB solutions for 8 hours in the dark and then decolorized by boiling ethanol (96%) for 10 minutes. The leaves were cooled to room temperature and preserved in fresh ethanol.

1.12 Herbivory Treatments

The Spodoptera litura larval eggs were originally obtained from Taiwan Agricultural Chemicals and Toxic Substances Research Institute (Taichung County, Taiwan). Thirty uniformly sized larvae of the first instar stage were used for the anti-insect bioassay study. The larvae were continuously fed with tomato leaves harvested from water or CAPE1 presprayed plants every 24 hours for 5 days. All larval weights were recorded for each day and the averages of larval weights were calculated. The larval sizes were observed after 5 days of feeding.

1.13 Pathogen Growth and Challenge

The bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) or Pst DC3000 hrcC⁻ were grown on King's B (KB) agar medium containing 100 mg/L rifampicin for 2 days at 28° C. Before the challenge, the bacteria were cultured in KB liquid medium at 28° C. with 230 rpm shaking overnight. The bacteria were pelleted by centrifugation and resuspended in 10 mM MgSO₄ at A600=0.25 (about 10⁸ cfu/ml). The plants were dipped into a diluted suspension of 10⁵ cfu/ml Pst DC3000 in 10 mM MgSO₄ containing 0.005% Silwet L-77 under vacuum for 30 seconds. Psi DC3000 or hrcC⁻ were grown in water- or peptide-treated plants for several days to observe the symptoms and then the bacteria were collected from the leaves and evaluated by bacterial titers according to a method outlined previously (Zimmerli et al., 2000).

1.14 Western Blot Analysis

Ten-day-old CAPE1oxCNYD or CAPE1oxCNAD seedlings were subjected to medium supplemented with or without different NaCl concentration and with or without 125 mM NaCl for various time points. The collected samples were crushed with YSZ Grinding Media (FE-TEC, EZEAG0500) in 2 mL eppendorf tubes by sonication (KURABO, SH-48). During the preparation, the samples were submerged in liquid nitrogen for rapid freezing. The samples were then homogenized in extraction buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 20 mM EDTA, 1% [w/v] SDS and 10% [v/v] glycerol) at 95° C. for 5 min After centrifuging at 12,000 rpm for 10 min, the supernatant was transferred to a new eppendorf tube. Fifty micrograms of total proteins were loaded on 10% SDS-polyacrylamide gels and analyzed by western blotting. The recombinant PROAtCAPE1 tagged eYFP was detected by anti-GFP antibody (Roche; 11814460001), and horseradish peroxidase-conjugated anti-mouse antibody (Invitrogen; 616520) was used as a secondary antibody. To confirm the equal loading of total proteins, an anti-α-tubulin antibody (Sigma-Aldrich; T5168) was subsequently used to probe the same blot.

1.15 Accession Numbers

Sequence data from this article can be found in the International Tomato Annotation Group (ITAG) protein database or Genbank/EMBL databases. Sequence data of putative CAPE peptides in Arabidopsis from this article can be found in the Arabidopsis Genome Initiative under the following accession numbers: AT4033730.1, AT4G25780.1, AT4G33720.1, AT4G25790.1, AT5G57625.1, AT4G30320.1, AT2G14580.1 (PRB1), AT5G26130.1 and AT2G14610.1 (PR1).

2. Results

2.1 Identification of Wounding- Plus MeJA-Induced Peptides in Tomato Leaves

Quantitative analysis revealed a novel peptides and a known peptide (systemin) which showed no significant expression in the unwounded plant but was highly expressed after wounding plus MeJA treatment. The novel peptide derived from pathogenesis-related protein 1b (PR-1b) showed a similar expression response to systemin. Since PR-1b is classified as a member of the cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins (CAP) superfamily (Gibbs et al., 2008), this peptide was designated as CAP-derived peptide 1 (CAPE1). In CAPE1 identification, with the exception of the y1 and b1 ions, most of the y and b fragment ions were matched to the theoretical fragments of the CAPE1 sequence. Using this approach, the tissue quantity used for global peptide identification was <150 g. To confirm the matched sequences, synthetic CAPE1 was analyzed by MS/MS and the resulting spectrum was totally matched to the endogenous CAPE1. Without peptide pre-fractionation, total peptides extracted from the unwounded, mechanically wounded and wounded plus MeJA treated tomato plants were directly analyzed by nanoUHPLC-SRM-MS targeted on the specific CAPE1 collisional induced dissociation (CID) reaction. The quantitation result showed that CAPE1 was expressed in low level in unwounded plants but significantly induced after wounding or wounding plus MeJA treatments (FIG. 1).

2.2 Bioactivity of CAPE1

CAPE1 treatment induces H₂O, formation in tomato leaves as detected by DAB staining (FIG. 2). The profiles of induced genes obtained by microarray analysis suggest that CAPE1 elevates the expression of several genes known to be involved in the anti-herbivore and anti-pathogen defense response. CAPE1 mainly induced genes involved in the stress response, defense response, innate immune response, bacterial defense and systemic acquired resistance (SAR). Reverse transcription quantitative PCR (qRT-PCR) analysis further confirmed that the anti-herbivore genes PROTEINASE INHIBITOR 1 and 2 (PI-1 and PI-2) and pathogen-related genes PATHOGENESIS-RELATED PROTEIN 1b (PR-1b, CAPE1 precursor gene), BETA-1,3-GLUCANASE (PR-2), CYS PROTEASE (PR-7), CLASS II CHITINASE (Chi2; 1), ETHYLENE RESPONSE FACTOR 5 (ERF5) and AvrPto-DEPENDENT Pto-INTERACTING PROTEIN 3 (Adi3) were activated after CAPE1 treatment (FIG. 3).

The anti-herbivore response was evaluated by average larval weights of 30 Spodoptera litura larvae fed with tomato leaves pretreated with water or CAPE1. Tomato plants pre-sprayed with CAPE1 suppressed larval growth and reduced larval weight by about 20% (FIG. 4a ). To demonstrate that plant resistance can also be enhanced by CAPE1, two groups of tomato plants were pre-sprayed with water or synthetic CAPE1 for 2 hours. After the treatment, the two plant groups underwent challenge with the pathogen Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). As shown in FIG. 4b , the water pretreated tomato plants showed severe pathogen infection symptoms.

To compare the anti-herbivore response of systemin with CAPE1, excised tomato plants were used, since the excised plant treated with peptide solution has been used previously to test the bioactivity of systemin (Schaller et al., 1995; Howe et al., 1996). JA and JA-Ile were observed to be significantly induced by treatment for 2 hours with systemin, but was induced after 4 hours treatment with CAPE1, and the expression level was ˜4 fold lower than that of systemin (FIG. 5). As the results suggested that CAPE1 may be a novel DAMP signal for the induction of immunity to pathogenesis, next, CAPE1 was compared with the canonical Pathogen/Microbe Associated Molecular Pattern (PAMP/MAMP) peptide “flg22” (Hayashi et al., 2001). As shown in FIG. 6a , both CAPE1 and flg22 significantly induced SA when supplied to excised plants. In FIG. 6b , the flg22 highly induced WRKY TRANSCRIPTION FACTOR 53 (WRKY53) expression but not PR-1b in tomato. This result was consistent with the public RNA-seq data in the Tomato Functional Genomics Database (TFGD) (Fei et al., 2011), which are based on the experiment “transcriptome sequencing of tomato leaves treated with different bacteria and PAMPs” (Rosli et al., 2013). The RNA-seq data showed that WRKY53 could be induced but PR-1b, Adi3 and ERF5, but could not be significantly induced using 30 minute or 6 hours treatment of flg22 on the tomato. However, the CAPE1 did not induce WRKY53 but highly induced its precursor gene PR-1b. Spraying of plants for 2 hours with either CAPE1 or flg22 resulted in plant resistance to Pst DC3000 infection (FIG. 6c ). The anti-pathogen responses including the SA biosynthesis and defense gene (ERF5 and PR-1b) expression can be induced by CAPE1 systemically. This data shows that the CAPE1 is a signaling peptide for regulating not only local but also systemic defense response throughout the whole plant (FIG. 7)

2.3 CAPE1 Proprotein

The mature CAPE1 peptide is derived from the C-terminal end of tomato PR-1b. This proprotein consists of an N-terminal signal peptide, a CAP domain and an extended C-terminal end (FIG. 8a ). The phylogenetic analysis using Molecular Evolutionary Genetics Analysis version 5.2 (MEGA5.2)(Tamura et al., 2011) and C-terminal alignment of the PR-1b protein demonstrated that the full protein and extended C-terminal end are highly conserved across different flowering plants ranging from monocots to dicots (FIG. 8b ). It is interesting that the PxGNxxxxxPY-motif (SEQ ID NO: 1) was conserved in the CAPE1 sequence, and also that the three residue sequences before the cleavage site had a conserved CNYx motif (SEQ ID NO: 55) (FIG. 8c ). This suggests that CNYx.PxGNxxxxxPY- (SEQ ID NO: 28) could be a functional motif that may mark bioactive peptides in other species.

2.4 CAPE Peptides in Arabidopsis

To demonstrate that a peptide derived from the CNYx.PxGNxxxxxPY-motif (SEQ ID NO: 28) could be bioactive, the Arabidopsis CAPE homologs, AtCAPE1 and AtCAPE9 were selected. AtCAPE1 and AtCAPE9 have highest and lowest sequence identity compared with SolCAPE1. Both peptides were shown to increase immunity against Pst DC3000 infection (FIG. 9). To confirm this proteolytic process of the AtCAPE1 precursor, we generated a transgenic plant, CAPE1oxCNYD, where wild-type PROAtCAPE1 fused with C-terminal enhanced yellow fluorescent protein (eYFP) was constitutively overproduced by the 35S promoter. This data shows that the MWs of the two bands were close to that of the precursor protein tagged with eYFP (45.76 kDa) and the AtCAPE1 fused to eYFP (26.3 kDa), respectively, when the cleavage occurred at the predicted cleavage site (FIGS. 10a and 10b ). In Arabidopsis, the salt treatment can induce AtCAPE1 production and even trigger the AtCAPE1 transportation from root to shoot (FIG. 10c ). The salt treatment also can enhance the anti-pathogen activity in Arabidopsis (FIG. 11), which may due to the CAPE1 production and transportation can be induced by salt stress. This result shows that the movement of CAPE peptides for regulating systemic immune responses.

2.5 the Importance of Conserved Cleavage Motif

To confirm the importance of conserved cleavage motif, we then generated transgenic lines, named CAPE1oxCNAD, where eYFP was fused with PROAtCAPE1 but with a mutation (Y160A) in the CNYx motif. We then examined expression of the mutated PROAtCAPE1-eYFP. Only a single band with a MW of 45.76 kDa was detected in all three independent transgenic lines (FIG. 12). These results suggested that the identified AtCAPE1 was derived from its precursor, PROAtCAPE1, through cleavage at the conserved CNYx motif (SEQ ID NO: 55), and that an aromatic amino residue, tyrosine, is important for the process. We also used the conserved CNYx motif (SEQ ID NO: 55) for designing protease inhibitor to prevent process in tomato. The result showed that the defense gene expression was decreased after the treatment of CNYDPV to tomato plants (FIG. 13).

3. Discussion

In this study, quantitative peptidomics analysis revealed three peptides, including systemin, that were not significantly expressed in the unwounded plant but were expressed at high levels after wounding plus MeJA treatment. This peptide is a signaling molecule for the systemic activation of the anti-herbivore response (Pearce et al., 1991). Systemin is the upstream component of the anti-herbivore signaling cascade and systemic signal transmission is mediated by jasmonic acid (JA) (Li et al., 2003; Stratmann, 2003). We show here the concentration change of endogenous systemin, a well-known wound-induced peptide, before and after the induction of wounding plus MeJA treatment. The detection of systemin also proved that the platform proposed in this study is able to detect defense signaling peptides. The second peptide found to be up-regulated upon treatment was derived from the chloroplast photosystem II subunit X. This peptide may be associated with the induction of reactive oxygen species (ROS) in chloroplasts. The third peptide (designated as CAPE1) was derived from pathogenesis-related protein 1b (PR-1b), a protein of unclear function.

The H₂O₂ and defense gene responses induced by CAPE1 indicated that this peptide regulates plant defense responses. H₂O₂ is a ROS involved in several defense responses during wounding, insect attacks and pathogen infections (Doke et al., 1996; Lamb and Dixon, 1997; Orozco-Cardenas and Ryan, 1999). CAPE1 was shown to be a DAMP elicitor in this study as it was induced by wounding and activated defense responses. Although several peptides in tomato are proposed to be DAMPs, the evidence for a peptide DAMP is mainly based on the consideration of the precursor gene induced by the damage or the bioactivity of synthesized putative peptides (Pearce et al., 1991; Huffaker et al., 2006; A. P. Trivilin, 2014). Microarray and qRT-PCR analysis showed that CAPE1 can induce defense genes to produce immune responses against herbivores and pathogens. Both JA and SA hormones can be induced by CAPE1, which explains why anti-herbivore and anti-pathogen genes were induced by the peptide treatment. The JA and SA biosynthesis pathways are known to be antagonistic (Robert-Seilaniantz et al., 2011; Thaler et al., 2012) but they may also function synergistically in the SA-JA-ethylene backbone of the plant immune signaling network, thereby redirecting defense output (Verhage et al., 2010). In comparison with the activation of anti-herbivore and anti-pathogen responses by systemin and flg22, respectively, CAPE1 showed a mild anti-herbivore response but activated a comparable anti-pathogen response. The mild anti-herbivore response induced by CAPE1 can be explained by a lower induction level of PI genes and JA hormones than that seen with systemin treatment. CAPE1 significantly induced several pathogen-related marker genes, including PR-2, PR-7, Chi2; 1 and the precursor of CAPE1 (PR-1b). Unlike flg22, which induces WRKY53 (Xiao et al., 2007), the CAPE1 triggered immunity did not induce the PTI responsive gene WRKY53 but induced PR-1b. This implies that flg22 and CAPE1 respectively act as an elicitor for PAMP/MAMP and DAMP and thereby regulate different mechanisms in the anti-pathogen response. In addition, ERF5, a GCC box (AGCCGCC) binding protein, was induced by CAPE1. We suggest that ERF5 is a mediator of CAPE1 defense responses because of the GCC box, a cis-acting element found in the promoter of many jasmonic acid (JA)/ethylene (ET)-inducible and PR genes. ERF5 was also demonstrated to positively regulate SA signaling and plant immunities against the bacterial pathogen Pst DC3000 and improve plant resistance to pathogens by activating several PR genes (Moffat et al., 2012; Son et al., 2012). In tomato, the overexpression of ERF5 was observed to induce PR genes and conferred tolerance to Ralstonia solanacearum (Li et al., 2011). This study suggested an alternative approach to enhance plant resistance through ERF5, which can be regulated by a low concentration of peptide without the use of transgenes. Furthermore, Adi3, encoding a component of the effector-triggered immunity (ETI) response, which negatively regulates programmed cell death (PCD) (Devarenne et al., 2006), was induced after CAPE1 treatment. Adi3 is a cell death suppressor (CDS) and its localization is dictated by a nuclear localization signal found in the Adi3 T-loop extension, which is phosphorylated for kinase activation (Ek-Ramos et al., 2010b). The deactivation of Adi3 CDS function is initiated by the interaction of Pto only when Pto interacts with the Pst effector protein AvrPto. This deactivation of CDS activity can lead to HR, which functions to limit pathogen spread. The HR through deactivation of Adi3 function was demonstrated to be compensated for by overexpression of Adi3 (Devarenne et al., 2006; Ek-Ramos et al., 2010a). In this study, CAPE1 was found to activate a “defense-no-death” phenotype to enhance plant resistance against the bacterial pathogen Pst DC3000 without induction of the HR (Yu et al., 1998). This phenotype could be explained by the elevated level of transcription of anti-pathogen and cell death suppressor genes as well as the level of SA. It also suggests that systemically induced immune responses can be activated by CAPE1, since SA and TA are essential hormones for the induction of SAR and induced systemic resistance (ISR), respectively (Pieterse et al., 2009). Plant insects and pathogens are responsible for substantial crop losses worldwide every year, and amid increasing environmental concerns, the use of agrochemicals to defeat the biological stress is more and more restricted. CAPE1 may potentially be used to activate resistance against biological threats in tomato. Furthermore, the highly conserved sequence of CAPE1 and its proprotein suggests that CAPE1 may also exist and be biologically active in other species. This study demonstrated the role of PR-1b in tomato defense signaling, and also demonstrated that the putative CAPE peptides with a PxGNxxxxxPY-motif (SEQ ID NO: 1) derived from Arabidopsis induces resistance against Pst DC3000 in Arabidopsis. Otherwise, the salt treatment can induce the AtCAPE1 production and transportation from root to shoot. This result indicates that the role of CAPE peptides for systemic immune regulation in diverse plant species. The conserved cleavage motif CNYx (SEQ ID NO: 55) was also identified as an important sequence for the plant immunity by regulating the process. Although At-PR1 is considered to be a common marker gene for the anti-pathogen response, its function was unclear previously. This study highlights the biological role of PR1 and CAP proteins in systemic defense signaling.

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1-19. (canceled)
 20. An isolated plant defense signaling polypeptide comprising a motif of SEQ ID NO: 1 or 28, wherein the polypeptide has up to 100 amino acids.
 21. The polypeptide of claim 20, wherein the polypeptide has up to 50 amino acids in length.
 22. The polypeptide of claim 20, wherein the polypeptide has up to 40 amino acids in length.
 23. The polypeptide of claim 20, wherein the polypeptide has up to 30 amino acids in length.
 24. The polypeptide of claim 20, wherein the polypeptide has up to 15 amino acids in length peptide
 25. The polypeptide of claim 20, wherein the polypeptide consists of SEQ ID NO: 1 or SEQ ID NO:
 28. 26. The polypeptide of claim 20, wherein the polypeptide is selected from the group consisting of SEQ ID NO: 2-27 and SEQ ID NO: 29-54.
 27. A composition comprising an isolated plant defense signaling polypeptide of claim
 20. 28. The composition of claim 27, further comprising salt.
 29. The composition of claim 27, wherein the polypeptide is present in the composition in an amount effective in inducing systemic immune responses in a plant.
 30. The composition of claim 29, wherein the polypeptide is present in the composition at a concentration of 50 nM to 250 nM.
 31. The composition of claim 29, wherein the systemic immune responses are selected from the group consisting of production of hydrogen peroxide (H₂O₂), generation of a plant hormone, and expression of an anti-herbivore or anti-pathogen protein.
 32. The composition of claim 31, wherein the plant hormone is selected from the group consisting of jasmonate (JA), JA conjugated with amino acid isoleucine (JA-Ile), and salicylic acid (SA).
 33. The composition of claim 31, wherein the anti-herbivore or anti-pathogen protein is selected from the group consisting of proteinase inhibitor 1 (PI-1), proteinase inhibitor 2 (PI-2), pathogenesis-related protein 1b (PR-1b, CAPE1 precursor gene), beta-1,3-glucanase (PR-2), cys protease (PR-7), class ii chitinase (Chi2;1), ethylene response factor 5 (ERF5), and avrpto-dependent pto-interacting protein 3 (Adi3).
 34. The composition of claim 27, further comprising an agriculturally acceptable carrier.
 35. The composition of claim 27, wherein the composition is an agricultural composition. 